Omics in Plant Breeding

Computational and high-throughput methods, such as genomics,
proteomics, and transcriptomics, known collectively as
"-omics," have been used to study plant biology for
well over a decade now. As these technologies mature, plant and
crop scientists have started using these methods to improve crop
varieties. Omics in Plant Breeding provides a timely introduction
to key omicsbased methods and their application in plant
breeding.

Omics in Plant Breeding is a practical and accessible
overview of specific omics-based methods ranging from metabolomics
to phenomics. Covering a single methodology within each chapter,
this book provides thorough coverage that ensures a strong
understanding of each methodology both in its application to, and
improvement of, plant breeding.

Accessible to advanced students, researchers, and professionals,
Omics in Plant Breeding will

be an essential entry point into this innovative and exciting
field.

• A valuable overview of high-throughput, genomics-based
  technologies and their applications to plant breeding

• Each chapter explores a single methodology, allowing for
  detailed and thorough coverage

• Coverage ranges from well-established methodologies,
  such as genomics and proteomics, to emerging technologies,
  including phenomics and physionomics

Aluízio Borém is a Professor of Plant Breeding
at the University of Viçosa in Brazil.

Roberto Fritsche-Neto is a Professor of Genetics and
Plant Breeding at the University of São Paulo in Brazil.

Autorentext

Aluzio Borem de Olieviera is a Professor of Crop Science at the University of Viçosa in Brazil. Prof. Borem received his Ph.D from the University of Minnesota. He has written, or contributed to, more than 50 books in his career.

Roberto Fritsche-Neto is an Adjunct Professor of Crop Science at the University of Viçosa in Brazil. Dr. Fritsche-Neto has co-edited two volumes, Plant Breeding for Biotic Stress Resistance and Plant Breeding for Abiotic Stress Resistance. Both published by Springer in 2012.

Zusammenfassung

Computational and high-throughput methods, such as genomics, proteomics, and transcriptomics, known collectively as -omics, have been used to study plant biology for well over a decade now. As these technologies mature, plant and crop scientists have started using these methods to improve crop varieties. Omics in Plant Breeding provides a timely introduction to key omicsbased methods and their application in plant breeding.

Omics in Plant Breeding is a practical and accessible overview of specific omics-based methods ranging from metabolomics to phenomics. Covering a single methodology within each chapter, this book provides thorough coverage that ensures a strong understanding of each methodology both in its application to, and improvement of, plant breeding.

Accessible to advanced students, researchers, and professionals, Omics in Plant Breeding will
be an essential entry point into this innovative and exciting field.

• A valuable overview of high-throughput, genomics-based technologies and their applications to plant breeding

• Each chapter explores a single methodology, allowing for detailed and thorough coverage

• Coverage ranges from well-established methodologies, such as genomics and proteomics, to emerging technologies, including phenomics and physionomics

Aluízio Borém is a Professor of Plant Breeding at the University of Viçosa in Brazil.

Roberto Fritsche-Neto is a Professor of Genetics and Plant Breeding at the University of São Paulo in Brazil.

Inhalt
List of Contributors ix Foreword xiii

1 Omics: Opening up the "Black Box" of the Phenotype 1
Roberto Fritsche-Neto and Aluizio Borem

The Post-Genomics Era 3

The Omics in Plant Breeding 4

Genomics, Precision Genomics, and RNA Interference 5

Transcriptomics and Proteomics 8

Metabolomics and Physiognomics 8

Phenomics 9

Bioinformatics 10

Prospects 10

References 10

2 Genomics 13
Antonio Costa de Oliveira, Luciano Carlos da Maia, Daniel da Rosa Farias, and Naciele Marini

The Rise of Genomics 13

DNA Sequencing 13

Development of Sequence-based Markers 18

Genome Wide Selection (GWS) 25

Structural and Comparative Genomics 27

References 28

3 Transcriptomics 33
Carolina Munari Rodrigues, Valeria S. Mafra, and Marcos Antonio Machado

Methods of Studying the Transcriptome 34

Applications of Transcriptomics Approaches for Crop Breeding 46

Conclusions and Future Prospects 51

Acknowledgements 51

References 51

4 Proteomics 59
Ilara Gabriela F. Budzinski, Thais Regiani, Monica T. Veneziano Labate, Simone Guidetti-Gonzalez, Danielle Izilda R. da Silva, Maria Juliana Calderan Rodrigues, Janaina de Santana Borges, Ivan Miletovic Mozol, and Carlos Alberto Labate

History 59

Different Methods for the Extraction of Total Proteins 60

Subcellular Proteomics 64

Post-Translational Modifications 66

Quantitative Proteomics 69

Perspectives 72

References 73

5 Metabolomics 81
Valdir Diola (in memoriam), Danilo de Menezes Daloso, and Werner Camargos Antunes

Introduction 81

Metabolomic and Biochemical Molecules 83

Technologies for Metabolomics 83

Metabolomic Database Analysis 86

Metabolomics Applications 89

Metabolomics-assisted Plant Breeding 91

Associative Genome Mapping and mQTL Profiles 95

Large-scale Phenotyping Using Metabolomics 97

Conclusion and Outlook 98

References 99

6 Physionomics 103
Frederico Almeida de Jesus, Agustin Zsogon, and Lazaro Eustaquio Pereira Peres

Introduction 103

Early Studies on Plant Physiology and the Discovery of Photosynthesis 104

Biochemical Approaches to Plant Physiology and the Discovery of Plant Hormones 104

Genetic Approaches to Plant Physiology and the Discovery of Hormone Signal Transduction Pathways 106

Alternative Genetic Models for Omics Approaches in Plant Physiology 112

"Physionomics" as an Integrator of Various Omics for Functional Studies and Plant Breeding 117

Acknowledgements 121

References 121

7 Phenomics 127
Roberto Fritsche-Neto, Aluizio Borem, and Joshua N. Cobb

Introduction 127

Examples of Large-scale Phenotyping 128

Important Aspects for Phenomics Implementation 134

Main Breeding Applications 141

Final Considerations 144

References 144

8 Electrophoresis, Chromatography, and Mass Spectrometry 147
Thais Regiani, Ilara Gabriela F. Budzinski, Simone Guidetti-Gonzalez, Monica T. Veneziano Labate, Fernando Cotinguiba, Felipe G. Marques, Fabricio E. Moraes, and Carlos Alberto Labate

Introduction 147

Two-dimensional Electrophoresis (2DE) 148

Chromatography 150

Mass Spectrometry 155

Data Analysis 161

References 164

9 Bioinformatics 167
J. Miguel Ortega and Fabricio R. Santos

Introduction 167

The "Omics" Megadata and Bioinformatics 167

Hardware for Modern Bioinformatics 169

Software for Genomic Sequencing 170 Software for Contig Asse...